We obtained the preprocessed `emp_deblur_150bp.subset_2k.rare_5000' dataset, describing a subset of the environmental 16S rRNA gene sequences from the Earth Microbiome Project [1]}, EMP, accessed via ftp://ftp.microbio.me/emp/. Communities from the EMP were mapped to our diffusion space using the following procedure: First, we generated a BLAST [2]} reference database of predicted 16S rRNA gene sequences for our set of RefSeq genomes using barrnap (https://github.com/tseemann/barrnap) to identify and retain the first instance of this ribosomal gene. The DECIPHER library in R was used to align sequences [3]}. We then conducted a BLAST sequence similarity search [2]} to match denoised sequence variants present in each EMP sample to the BLAST database and retained the top hits. Niches – operationally defined as the strategies describing the 10 taxa with the highest (positive) and lowest (negative) entries along each diffusion variable – were said to be `occupied' by taxa in an EMP community census if at least one detected sequence variant exhibited a 97% or greater rRNA gene sequence similarity to any of the extremal genomes. The results of this procedure were summarized as plots of the proportion of samples within each EMP `env_feature' category satisfying this criterion. Groupings of similar ecosystem types were accomplished using the Ward linkage method [5]} for hierarchical clustering.
